Qian Liu
| Snapshot Date: 2025-11-06 13:40 -0500 (Thu, 06 Nov 2025) |
| git_url: https://git.bioconductor.org/packages/ReUseData |
| git_branch: devel |
| git_last_commit: 4a5d06b |
| git_last_commit_date: 2025-10-29 11:20:44 -0500 (Wed, 29 Oct 2025) |
| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-11-07 11:32 -0500 (Fri, 07 Nov 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4818 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 1746/2323 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| ReUseData 1.11.0 (landing page) Qian Liu
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
|
To the developers/maintainers of the ReUseData package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/ReUseData.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: ReUseData |
| Version: 1.11.0 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz |
| StartedAt: 2025-11-07 02:55:36 -0500 (Fri, 07 Nov 2025) |
| EndedAt: 2025-11-07 02:58:21 -0500 (Fri, 07 Nov 2025) |
| EllapsedTime: 164.2 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: ReUseData.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD check --install=check:ReUseData.install-out.txt --library=/home/biocbuild/bbs-3.23-bioc/R/site-library --timings ReUseData_1.11.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘ReUseData/DESCRIPTION’ ... OK
* this is package ‘ReUseData’ version ‘1.11.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘ReUseData’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
dataHub-class 6.261 0.515 6.778
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.23-bioc/meat/ReUseData.Rcheck/00check.log’
for details.
ReUseData.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL ReUseData ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’ * installing *source* package ‘ReUseData’ ... ** this is package ‘ReUseData’ version ‘1.11.0’ ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (ReUseData)
ReUseData.Rcheck/tests/testthat.Rout
R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(testthat)
> library(ReUseData)
>
> test_check("ReUseData")
Note: you need to assign a name for the recipe: rcpName <- recipeLoad('xx')
Data recipe loaded!
Use inputs() to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/echo_out.html
for user instructions (e.g., eligible input values, data source, etc.)
}[1;30mINFO[0m Final process status is success
Updating data record...
outfile.txt added
Updating data record...
2ef60b61ae05e_GRCh38.primary_assembly.genome.fa.1.bt2 added
2ef60b3f18128f_GRCh38.primary_assembly.genome.fa.2.bt2 added
2ef60b4ac5caa1_GRCh38.primary_assembly.genome.fa.3.bt2 added
2ef60b36200fdb_GRCh38.primary_assembly.genome.fa.4.bt2 added
2ef60b4a7e20c6_GRCh38.primary_assembly.genome.fa.rev.1.bt2 added
2ef60b49766e4f_GRCh38.primary_assembly.genome.fa.rev.2.bt2 added
2ef60b7fade7ed_outfile.txt added
2ef60b580c9403_GRCh37_to_GRCh38.chain added
2ef60b755ef825_GRCh37_to_NCBI34.chain added
2ef60b23e072b3_GRCh37_to_NCBI35.chain added
2ef60b5a4c9d09_GRCh37_to_NCBI36.chain added
2ef60b4f38afc4_GRCh38_to_GRCh37.chain added
2ef60b5d67866c_GRCh38_to_NCBI34.chain added
2ef60b46fb4cdd_GRCh38_to_NCBI35.chain added
2ef60bc0bfeaf_GRCh38_to_NCBI36.chain added
2ef60b4251dfb3_NCBI34_to_GRCh37.chain added
2ef60b5ee13c44_NCBI34_to_GRCh38.chain added
2ef60b653acc77_NCBI35_to_GRCh37.chain added
2ef60b181fee17_NCBI35_to_GRCh38.chain added
2ef60b3339a967_NCBI36_to_GRCh37.chain added
2ef60b6396f08e_NCBI36_to_GRCh38.chain added
2ef60b494e7100_GRCm38_to_NCBIM36.chain added
2ef60b200c13ab_GRCm38_to_NCBIM37.chain added
2ef60b2a885417_NCBIM36_to_GRCm38.chain added
2ef60b29839ed8_NCBIM37_to_GRCm38.chain added
2ef60b31f70ba7_1000G_omni2.5.b37.vcf.gz added
2ef60b38635f46_1000G_omni2.5.b37.vcf.gz.tbi added
2ef60b368ae8d8_Mills_and_1000G_gold_standard.indels.b37.vcf.gz added
2ef60b6885fb23_Mills_and_1000G_gold_standard.indels.b37.vcf.gz.tbi added
2ef60b2b18d75f_1000G_omni2.5.hg38.vcf.gz added
2ef60b2599f1d3_1000G_omni2.5.hg38.vcf.gz.tbi added
2ef60b6ea0db82_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz added
2ef60b6a30e9ef_Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi added
2ef60b705fbc74_af-only-gnomad.raw.sites.vcf added
2ef60b24c0eb5d_af-only-gnomad.raw.sites.vcf.idx added
2ef60b34af0ab5_Mutect2-exome-panel.vcf.idx added
2ef60b39d62ac3_Mutect2-WGS-panel-b37.vcf added
2ef60b246ed34a_Mutect2-WGS-panel-b37.vcf.idx added
2ef60bcbb9eb8_small_exac_common_3.vcf added
2ef60b2f3522e8_small_exac_common_3.vcf.idx added
2ef60b484f45fd_1000g_pon.hg38.vcf.gz added
2ef60b67083bc1_1000g_pon.hg38.vcf.gz.tbi added
2ef60b7e6dd2ad_af-only-gnomad.hg38.vcf.gz added
2ef60b25b6cc69_af-only-gnomad.hg38.vcf.gz.tbi added
2ef60b2e03889e_small_exac_common_3.hg38.vcf.gz added
2ef60ba79d15c_small_exac_common_3.hg38.vcf.gz.tbi added
2ef60b6808ac1d_gencode.v41.annotation.gtf added
2ef60bce4c4e2_gencode.v42.annotation.gtf added
2ef60b6fb49dd3_gencode.vM30.annotation.gtf added
2ef60b289a34_gencode.vM31.annotation.gtf added
2ef60b401e6e49_gencode.v41.transcripts.fa added
2ef60b534b8e61_gencode.v41.transcripts.fa.fai added
2ef60b49770b35_gencode.v42.transcripts.fa added
2ef60b602a81f4_gencode.v42.transcripts.fa.fai added
2ef60b7dd3e278_gencode.vM30.pc_transcripts.fa added
2ef60b72faaa0d_gencode.vM30.pc_transcripts.fa.fai added
2ef60b12218d9c_gencode.vM31.pc_transcripts.fa added
2ef60b363741bf_gencode.vM31.pc_transcripts.fa.fai added
2ef60b298592e5_GRCh38.primary_assembly.genome.fa.1.ht2 added
2ef60b7aa788bf_GRCh38.primary_assembly.genome.fa.2.ht2 added
2ef60b6150191e_GRCh38.primary_assembly.genome.fa.3.ht2 added
2ef60b4f1f84b8_GRCh38.primary_assembly.genome.fa.4.ht2 added
2ef60b69486441_GRCh38.primary_assembly.genome.fa.5.ht2 added
2ef60b4b81030d_GRCh38.primary_assembly.genome.fa.6.ht2 added
2ef60b3f7f412c_GRCh38.primary_assembly.genome.fa.7.ht2 added
2ef60be094f9e_GRCh38.primary_assembly.genome.fa.8.ht2 added
2ef60b300dc2_GRCh38_full_analysis_set_plus_decoy_hla.fa.fai added
2ef60b79556bef_GRCh38_full_analysis_set_plus_decoy_hla.fa.amb added
2ef60b327822e8_GRCh38_full_analysis_set_plus_decoy_hla.fa.ann added
2ef60bcebac7a_GRCh38_full_analysis_set_plus_decoy_hla.fa.bwt added
2ef60b288a8ed8_GRCh38_full_analysis_set_plus_decoy_hla.fa.pac added
2ef60b7ac768e5_GRCh38_full_analysis_set_plus_decoy_hla.fa.sa added
2ef60b73f3e83b_GRCh38_full_analysis_set_plus_decoy_hla.fa added
2ef60b26f86185_GRCh38.primary_assembly.genome.fa.fai added
2ef60b207e354f_GRCh38.primary_assembly.genome.fa.amb added
2ef60b21f770d9_GRCh38.primary_assembly.genome.fa.ann added
2ef60b317232e1_GRCh38.primary_assembly.genome.fa.bwt added
2ef60b886e16c_GRCh38.primary_assembly.genome.fa.pac added
2ef60b2edc35bc_GRCh38.primary_assembly.genome.fa.sa added
2ef60b2126d0b5_GRCh38.primary_assembly.genome.fa added
2ef60b8af7ba0_hs37d5.fa.fai added
2ef60b6efaa405_hs37d5.fa.amb added
2ef60b74725f16_hs37d5.fa.ann added
2ef60b522686d5_hs37d5.fa.bwt added
2ef60b4f2525fa_hs37d5.fa.pac added
2ef60b7246418f_hs37d5.fa.sa added
2ef60b452130e3_hs37d5.fa added
2ef60b6146b396_complete_ref_lens.bin added
2ef60b287d834e_ctable.bin added
2ef60b6ea6c3c8_ctg_offsets.bin added
2ef60b5bee3c55_duplicate_clusters.tsv added
2ef60b9cd9c6c_info.json added
2ef60b3dc64881_mphf.bin added
2ef60b4536a097_pos.bin added
2ef60b554e9f7a_pre_indexing.log added
2ef60b7d4589ad_rank.bin added
2ef60b533ff035_ref_indexing.log added
2ef60b557ead3c_refAccumLengths.bin added
2ef60b769af59d_reflengths.bin added
2ef60b5b8131e_refseq.bin added
2ef60b626a59b7_seq.bin added
2ef60b1f258475_versionInfo.json added
2ef60b7f7c03_salmon_index added
2ef60b565e41f2_chrLength.txt added
2ef60b461de5fa_chrName.txt added
2ef60b20fdb152_chrNameLength.txt added
2ef60b7855b2cc_chrStart.txt added
2ef60b779018db_exonGeTrInfo.tab added
2ef60b298492be_exonInfo.tab added
2ef60b2731e888_geneInfo.tab added
2ef60b18b6e990_Genome added
2ef60b32340e5f_genomeParameters.txt added
2ef60b162c8c8d_Log.out added
2ef60bd2948a7_SA added
2ef60b45a9534_SAindex added
2ef60b6551b287_sjdbInfo.txt added
2ef60b7f6f8a36_sjdbList.fromGTF.out.tab added
2ef60b497bc617_sjdbList.out.tab added
2ef60b4698661d_transcriptInfo.tab added
2ef60b27ed0d84_GRCh38.GENCODE.v42_100 added
2ef60b382289e0_knownGene_hg38.sql added
2ef60b2286a273_knownGene_hg38.txt added
2ef60b31baa9f0_refGene_hg38.sql added
2ef60b75e8d261_refGene_hg38.txt added
2ef60b67bd430a_knownGene_mm39.sql added
2ef60b709496a_knownGene_mm39.txt added
2ef60b732e5c0e_refGene_mm39.sql added
2ef60b3afd333f_refGene_mm39.txt added
trying URL 'https://storage.googleapis.com/reusedata/echo/outfile.txt'
Content type 'text/plain' length 30 bytes
==================================================
downloaded 30 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.yml'
Content type 'application/x-yaml' length 151 bytes
==================================================
downloaded 151 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.cwl'
Content type 'application/octet-stream' length 1152 bytes
==================================================
downloaded 1152 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.md5'
Content type 'application/octet-stream' length 45 bytes
==================================================
downloaded 45 bytes
trying URL 'https://storage.googleapis.com/reusedata/echo/echo_out_Hello_World!_outfile.sh'
Content type 'application/x-shellscript' length 68 bytes
==================================================
downloaded 68 bytes
Data is downloaded:
/tmp/RtmpyRJOWD/test_gcpData/outfile.txt
}[1;30mINFO[0m Final process status is success
NOTE: existing caches will be removed and regenerated!
Updating recipes...
STAR_index.R added
bowtie2_index.R added
echo_out.R added
ensembl_liftover.R added
gcp_broad_gatk_hg19.R added
gcp_broad_gatk_hg38.R added
gcp_gatk_mutect2_b37.R added
gcp_gatk_mutect2_hg38.R added
gencode_annotation.R added
gencode_genome_grch38.R added
gencode_transcripts.R added
hisat2_index.R added
reference_genome.R added
salmon_index.R added
ucsc_database.R added
Data recipe loaded!
Use inputs(ensembl_liftover) to check required input parameters before evaluation.
Check here: https://rcwl.org/dataRecipes/ensembl_liftover.html
for user instructions (e.g., eligible input values, data source, etc.)
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 44 ]
> Sys.setenv(cachePath = file.path(tempdir(), "cache"))
>
>
>
> proc.time()
user system elapsed
17.705 1.139 19.453
ReUseData.Rcheck/ReUseData-Ex.timings
| name | user | system | elapsed | |
| dataHub-class | 6.261 | 0.515 | 6.778 | |
| dataSearch | 1.069 | 0.035 | 1.104 | |
| dataUpdate | 0 | 0 | 0 | |
| getCloudData | 2.481 | 0.108 | 3.453 | |
| getData | 0.000 | 0.001 | 0.001 | |
| meta_data | 0.000 | 0.001 | 0.001 | |
| recipeHub-class | 0.116 | 0.001 | 0.118 | |
| recipeLoad | 1.189 | 0.026 | 1.216 | |
| recipeMake | 0.000 | 0.000 | 0.001 | |
| recipeSearch | 0.513 | 0.009 | 0.522 | |
| recipeUpdate | 0 | 0 | 0 | |